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3D binning and geometry setup#

Create sparse 3D cube geometry by binning traces from 2D profiles.

Description#

This script uses the following processing steps to setup a 3D cube geometry and assign traces to each bin:

  1. Setup 3D geometry using
    • rotation center and angle
    • output cube extent (optionally with reference to study area extent)
  2. Transform coordinates of all 2D profiles (x,y → iline/xline) using Affine transformation
  3. Stack multiple traces within a single bin using
    • average amplitude
    • median amplitude
    • nearest trace(s) (calculated using spatial distance \(d\))
    • Inverse Distance Weighting (IDW) algorithm
  4. Create inline netCDF files from 2D profiles
  5. Merge all inlines into a single sparse 3D cube
  6. Transpose cube to time-major layout (il, xl, twt) → (twt, il, xl)

2D despike

Figure: Conceptual 3D binning process, where tr: trace, d: distance.

Suitable bin sizes

The bin sizes for a given dataset are largely dependent on (a) the line spacing and (b) the trace distance along individual lines. In case of survey lines with a predominant orientation, consider using an asymmetric bin size (e.g., 15 x 5 m).

Usage#

This script is designed to be used from the terminal (i.e. command line).

Command line interface#

The script can handle two different inputs:

  1. datalist of files to process (e.g., datalist.txt)
  2. directory with input files (e.g., /input_dir)

There are two options to run the script. We recommend using the CLI entry point like:

>>> 10_cube_geometry_binning {datalist.txt | </directory>} 
    --params_netcdf /path/to/config.yml
    --params_spatial_ref /path/to/spatial_ref.yml 
    --params_cube_setup /path/to/cube_setup.yml
    --path_coords {/path/to/segys/ | /path/to/auxiliary/file.nav}
    [optional parameters]

Alternatively, the script can be executed using the (more verbose) command:

>>> python -m pseudo_3D_interpolation.cube_binning_3D {datalist.txt | </directory>} 
    --params_netcdf /path/to/config.yml 
    --params_spatial_ref /path/to/spatial_ref.yml
    --params_cube_setup /path/to/cube_setup.yml
    --path_coords {/path/to/segys/ | /path/to/auxiliary/file.nav}
    [optional parameters]

Optionally, the following parameters can be specified:

  • --help, -h: Show help.

  • --params_netcdf: Path of netCDF parameter file (YAML format). Required!

  • --params_spatial_ref: Path of spatial reference parameter file with CRS as WKT string (YAML format). Required!

  • --params_cube_setup: Path of config file for cube geometry setup (YAML format). Required!

  • --output_dir {DIR}: Output directory for edited SEG-Y file(s).

  • --suffix {sgy}, -s: File suffix (default: sgy). Only used if directory is specified.

  • --filename_suffix {SUFFIX}: Filename suffix for guided selection (e.g. env or despk). Only used when input_path is a directory.

  • --attribute, -a:: Seismic attribute to compute.

  • --coords_origin {header | aux}: Origin of (shotpoint) coordinates (default: header).

  • --path_coords: Path to SEG-Y directory (coords_origin = header) or auxiliary navigation file with coordinates (coords_origin = aux). Required!

  • --coords_fsuffix: File suffix of auxiliary or SEG-Y files (depending on chosen parameter for coords_origin.

  • --bin_size: Bin size(s) in inline and crossline direction(s) given in CRS units (e.g., meter). Single value or space-separated inline and crossline values.

  • --twt_limits {MIN MAX}: Vertical two-way travel time range of output 3D cube (in ms).

  • --parallel: Process files in parallel (default: False)

  • --encode: Use encoding to compress output file size based on JSON parameter file (params_netcdf).

  • --stacking_method: Stacking method for multiple traces within one bin (default: average)

    • 'average', 'median', 'nearest', or 'IDW'

  • --factor_dist: Distance factor controlling the impact of weighting function: \(1/(distance^{factor})\). Only used if stacking_method=IDW.

  • --dtype_data: Output dtype of created 3D cube (default: float32).

  • --name: Optional identifier string to add to exported files.

  • --write_aux: Write auxiliary files featuring key cube parameters (default: False).

  • --verbose {LEVEL}, -V: Level of output verbosity (default: 0).

Configuration files#

netCDF parameter#

This config file specifies netCDF metadata information and is used in subsequent scripts as well.

# parameter for frequency domain
attrs_freq:
  data:
    description: Spectral amplitudes of frequency spectrum
    long_name: amplitude
    units: '-'
  new_dim:
    description: Frequencies of seismic signal
    long_name: frequency
    units: kHz
# parameter for time domain
attrs_time:
  amp:
    description: Measure of reflection strength of property contrast between layers
    long_name: seismic amplitude
    seismic_attribute: amplitude
    units: '-'
  cube:
    description: Sparse pseudo-3D cube created from TOPAS profiles
    history: ''
    long_name: central cube
  env:
    description: Phase-independent representation of seismic amplitude (instantaneous
      amplitude)
    long_name: signal envelope
    seismic_attribute: envelope
    units: '-'
  fold:
    description: Number of stacked traces per bin
    units: '#'
  iline:
    long_name: iline
    units: '#'
  twt:
    long_name: two-way travel time
    standard_name: TWT
    units: ms
  x:
    long_name: easting
    standard_name: projection_x_coordinate
    units: m
  xline:
    long_name: xline
    units: '#'
  y:
    long_name: northing
    standard_name: projection_y_coordinate
    units: m
encodings:
  amp:
    _FillValue: -32768
    dtype: int16
    scale_factor: 5.0e-05
  env:
    _FillValue: 0
    dtype: uint16
    scale_factor: 3.0e-05
# auxiliary netCDF variables
var_aux:
    - fold
    - ref_amp

Spatial reference#

The coordinate reference system (CRS) is specified as a WKT string in a separated YAML file. An example for WGS 84 / UTM zone 60S is shown below:

PROJCS["WGS 84 / UTM zone 60S",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",177],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",10000000],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["Easting",EAST],AXIS["Northing",NORTH],AUTHORITY["EPSG","32760"]]

3D cube setup parameter#

All required information for the geometry of the created 3D cube are specified in a designated YAML file. An example file might look like this:

# name of pseudo-3D cube
name: cube_center
long_name: central cube
# seismic attribute, e.g amplitude (amp), envelope (env)
attribute: amp
# bin size(s) for il/xl directions (in CRS units, e.g. meter)
bin_size: #5
  - 5   # iline bin size (along y-axis)
  - 5   # xline bin size (along x-axis)
# min/max TWT limits of output pseudo-3D cube (in ms)
twt_limits: 
  - 725
  - 925
# Stack multiple traces within a single bin using this method ('average', 'median', 'nearest', 'IDW')
stacking_method: IDW
factor_dist: 1.0    # only used if `stacking_method` == 'IDW'
# spatial reference of extent coordinates (should be identical to SEG-Y CRS)
spatial_ref: EPSG:32760
rotation_center: 
  - 297335 
  - 5125120
 # positive in clockwise direction (in degree)
rotation_angle: 12
# extent of the actual pseudo-3D cube to generate
extent_cube:
  lower_left: 
    - 296586.4282892714
    - 5123519.385932244
  upper_left:
    - 295994.9195288948
    - 5126302.215856332
  upper_right:
    - 298063.7017044469
    - 5126741.949082412
  lower_right:
    - 298655.2104648235
    - 5123959.119158324
# OPTIONAL: extent of the overall study area (must be larger than `extent_cube`)
extent_study_area:
  lower_left: 
    - 294112.69854084
    - 5120631.97166828
  upper_left:
    - 292594.94319787
    - 5127772.44915364
  upper_right:
    - 300664.66090393
    - 5129487.72060288
  lower_right:
    - 302182.4162469
    - 5122347.24311753
Last update: Monday, 03 July 2023 at 09:46:51